Selsey Coastguard and a Selsey RNLI lifeboat were called to the scene at around 12.30pm to the water off Mulberry at Pagham, where a passing paddle boarder had stopped to help.
Selsey RNLI said the pair, discovered approximately half a mile off shore and a mile east of Pagham yacht club, were both suffering from hypothermia.
The RNLI statement added: "The volunteer crew quickly spotted the paddle boarder who had been joined by a kayak and they had managed to get the boy out of the water. Apparently the vessel they were on sank and only the five year old had a buoyancy aid.
"The ILB (Selsey D class inshore lifeboat) came alongside the paddle boarder and recovered both the boy and his father.
"Both were given casualty care including oxygen. The father was exhausted and both of them were suffering from hypothermia and possibly consumed sea water so an ambulance was requested to meet the ILB at the Pagham yacht club.
"Both were taken to hospital for further checks."
Soon after the incident, Selsey Coastguard warned about the importance of life jackets and buoyancy aids.
Writing on their Facebook page, they said: "The five-year-old was wearing a buoyancy aid however the father wasn't, and was very lucky that there was a paddle boarder that had spotted them and was able to help them.
"The father was tired, exhausted and was also suffering from shock and had swallowed a lot of sea water.
"Lifejackets and buoyancy aids aren't just for kids and should be worn by everyone - it doesn't matter how good a swimmer you are! It could be the difference between life and death and they could save your life.
"In an emergency out at sea, on the beach or along the coast dial 999 and ask for the Coastguard! #999Coastguard #Volunteers #AlwaysOnCall."
RNLI Selsey reiterated these warnings, stressing that life jackets and buoyancy aids should 'always be worn when going afloat'.